ENT MERFISH Report
1.1 Overview
1.1.1 Sample Information
A brief sample information is generated from the submission table for the following analysis.
| Expt | Sample | Index | Case_Number | Sex | Age | HPV | Sample_Region | Genotype | Group | Region | DataPath | Clinic.comment | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5 | 2 | TT29258 | TT29258 | 3 | M | 47 | Positive | Right tongue cancer | TT | Tumor | region_0 | Y:_Imaging_data_2\202412061704_20241206ENT2925859ImmunOncoh500x03_VMSC00101 | right tongue cancer, involving the right hemitongue and base of tongue, cT4N2bM0 |
| 6 | 2 | NT29259 | NT29259 | 3 | M | 47 | Positive | Right tongue cancer | NT | Normal | region_1 | Y:_Imaging_data_2\202412061704_20241206ENT2925859ImmunOncoh500x03_VMSC00101 | right tongue cancer, involving the right hemitongue and base of tongue, cT4N2bM0 |
1.1.2 MERSCOPE Data Quality Summary
The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.
Generally, log10 transcript count > 4.0 in most area can be considered as a good quality standard for human tissue.
Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.